Abstract

Esophageal atresia with or without tracheoesophageal fistula (EA/TEF) is a relatively common birth defect often associated with additional congenital anomalies such as vertebral, anal, cardiovascular, renal and limb defects, the so-called VACTERL association. Yet, little is known about the causal genetic factors. Rare case reports of gastrointestinal anomalies in children with triple X syndrome prompted us to survey the incidence of structural and numerical changes of chromosome X in patients with EA/TEF. All available (n=269) karyotypes of our large (321) EA/TEF patient cohort were evaluated for X-chromosome anomalies. If sufficient DNA material was available, we determined genome-wide copy number profiles with SNP array and identified subtelomeric aberrations on the difficult to profile PAR1 region using telomere-multiplex ligation-dependent probe amplification. In addition, we investigated X-chromosome inactivation (XCI) patterns and mode of inheritance of detected aberrations in selected patients. Three EA/TEF patients had an additional maternally inherited X chromosome. These three female patients had normal random XCI patterns. Two male EA/TEF patients had small inherited duplications of the XY-linked SHOX (Short stature HOmeoboX-containing) locus. Patients were small for gestational age at birth (<P5) and had additional, mostly VACTERL associated, anomalies. Triple X syndrome is rarely described in patients with EA/TEF and no duplications of the SHOX gene were reported so far in these patients. As normal patterns of XCI were seen, overexpression of X-linked genes that escape XCI, such as the SHOX gene, could be pathogenic by disturbing developmental pathways.

Triple X syndrome and SHOX aberrations in patients with esophageal atresia/tracheoesophageal fistula (OA/TOF). (a) The HumanCytoSNP-12 chip (Illumina) showing an interstitial duplication of the PAR1 region (base pair position chrX: 248 968–1 229 976), including the SHOX gene in patient 4. The elevated log 2 ratio indicates the duplicated segment (green bar). (b) The HumanCytoSNP-12 chip result visualized in Biodiscovery Nexus CN6.1. The B-allele frequency of patient 4 is indicated in the enlarged right panel (purple bar, arrow). The shift from a heterozygous state (gray dots, 0.5) to a 0.33/0.66 frequency (purple dots) is indicative for a copy number change. Taken together with the raise in the log R, this state is indicative for a copy number gain. (c) Schematic presentation of the SHOX A and B transcripts (dark blue and brown), the conserved noncoding elements (blue),SHOX gene exons (green), SHOX qPCR (red) and SHOX regulatory elements described in literature (dark red), the SHOX duplications in patients 4 and 5 and their position compared the duplications observed in patients 1–4 in Thomas et al, Roos et al, the database of genomic variation and the duplication in LWD/ISS patients described by Benito-Sanz et al. The red lines indicate the length of the duplications, with a larger duplication in patient 4 (amplicons 1–13) and a SHOX duplication in patient 5 (amplicons 2–8) (). Both MLPA probes (orange) were duplicated in patients 4 and 5.